Package phase

Class Stage2Haps

java.lang.Object

phase.Stage2Haps

public class Stage2Haps
extends java.lang.Object

Class Stage2Haps stores phased genotypes.

Instances of Stage2Haps are thread-safe.

Constructor Summary

Constructors

Constructor	Description
Stage2Haps(PhaseData phaseData)	Constructs a new Stage2Haps instance from the specified data.

Method Summary

Modifier and Type	Method	Description
FixedPhaseData	fpd()	Returns the input data for phasing that is the same in each iteration.
void	setPhasedGT(int marker, int sample, int a1, int a2)	Sets the phased genotype if the specified marker was not phased in the first stage.
BasicGT	toBasicGT(int start, int end)	Returns a BasicGT instance containing phased genotypes for the specified markers.
GTRec[]	toGTRecs(int start, int end)	Returns a GTRec[] instance containing phased genotypes for the specified markers.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Stage2Haps

public Stage2Haps(PhaseData phaseData)

Constructs a new Stage2Haps instance from the specified data.

Parameters:

phaseData - the current genotype phase estimates and parameter values

Throws:

java.lang.NullPointerException - if phaseData == null

Method Detail

fpd

public FixedPhaseData fpd()

Returns the input data for phasing that is the same in each iteration.

Returns:

the input data for phasing that is the same in each iteration

setPhasedGT

public void setPhasedGT(int marker,
                        int sample,
                        int a1,
                        int a2)

Sets the phased genotype if the specified marker was not phased in the first stage. The contract for this method is unspecified if the specified alleles are inconsistent with this.fpd().targGT().

Parameters:

sample - a sample index

marker - a marker index

a1 - the first allele index

a2 - the second allele index

Throws:

java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.fpd().targGT().markers().size()

java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.fpd().targGT().samples().size()

java.lang.IndexOutOfBoundsException - if a1 < 0 || a1 >= this.fpd().targGT().markers().marker(marker).nAlleles()

java.lang.IndexOutOfBoundsException - if a2 < 0 || a2 >= this.fpd().targGT().markers().marker(marker).nAlleles()

toBasicGT

public BasicGT toBasicGT(int start,
                         int end)

Returns a BasicGT instance containing phased genotypes for the specified markers.

Parameters:

start - the starting marker index (inclusive)

end - the ending marker index (exclusive)

Returns:

a BasicGT instance containing phased genotypes for the specified range of marker indices

Throws:

java.lang.IndexOutOfBoundsException - if start < 0 || end > this.nMarkers()

java.lang.IllegalArgumentException - if start >= end

toGTRecs

public GTRec[] toGTRecs(int start,
                        int end)

Returns a GTRec[] instance containing phased genotypes for the specified markers.

Parameters:

start - the starting marker index (inclusive)

end - the ending marker index (exclusive)

Returns:

a GTRec[] instance containing phased genotypes for the specified range of marker indices

Throws:

java.lang.IndexOutOfBoundsException - if start < 0 || end > this.nMarkers()

java.lang.IllegalArgumentException - if start >= end